The goal of this study was to compare two different methods for extracting bacterial and human proteins from human fecal material. Generally the LC-MS raw spectra are cleaner from the differential method with less non-peptide interference. The raw spectra from the direct method tend to have more dominant peptide peaks arising from very abundant human proteins. The differential centrifugation method provides a deeper look into the bacterial community. From all 20 microbes included in the database search Bacteriodes was the most heavily impacted by the extraction type with almost twice the number of spectra from the differential method (Figure 6). Many bacterial species were not effected by the extraction method.
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